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The Apache WSS4J project provides a Java implementation of the primary security standards for Web Services, namely the OASIS Web Services Security (WS-Security) specifications from the OASIS Web Services Security TC.
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/**
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements. See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership. The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License. You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied. See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */

package org.apache.ws.security.action;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.ws.security.WSSecurityException;
import org.apache.ws.security.components.crypto.Crypto;
import org.apache.ws.security.handler.RequestData;
import org.apache.ws.security.handler.WSHandler;
import org.apache.ws.security.handler.WSHandlerConstants;
import org.apache.ws.security.saml.SAMLIssuer;
import org.apache.ws.security.saml.SAMLIssuerFactory;
import org.apache.ws.security.saml.WSSecSignatureSAML;
import org.opensaml.SAMLAssertion;
import org.w3c.dom.Document;

public class SAMLTokenSignedAction implements Action {
    
    private static Log log = LogFactory.getLog(SAMLTokenSignedAction.class.getName());

    public void execute(WSHandler handler, int actionToDo, Document doc, RequestData reqData)
            throws WSSecurityException {
        Crypto crypto = null;
        /*
        * it is possible and legal that we do not have a signature
        * crypto here - thus ignore the exception. This is usually
        * the case for the SAML option "sender vouches". In this case
        * no user crypto is required.
        */
        try {
            crypto = handler.loadSignatureCrypto(reqData);
        } catch (Throwable t) {
            if (log.isDebugEnabled()) {
                log.debug(t.getMessage(), t);
            }
        }

        SAMLIssuer saml = loadSamlIssuer(handler, reqData);
        saml.setUsername(reqData.getUsername());
        saml.setUserCrypto(crypto);
        saml.setInstanceDoc(doc);

        SAMLAssertion assertion = saml.newAssertion();
        if (assertion == null) {
            throw new WSSecurityException("WSHandler: Signed SAML: no SAML token received");
        }
        String issuerKeyName = null;
        String issuerKeyPW = null;
        Crypto issuerCrypto = null;

        WSSecSignatureSAML wsSign = new WSSecSignatureSAML();
        wsSign.setWsConfig(reqData.getWssConfig());

        String password = null;
        if (saml.isSenderVouches()) {
            issuerKeyName = saml.getIssuerKeyName();
            issuerKeyPW = saml.getIssuerKeyPassword();
            issuerCrypto = saml.getIssuerCrypto();
        } else {
            password =
                    handler.getPassword(reqData.getUsername(),
                            actionToDo,
                            WSHandlerConstants.PW_CALLBACK_CLASS,
                            WSHandlerConstants.PW_CALLBACK_REF, reqData)
                            .getPassword();
            wsSign.setUserInfo(reqData.getUsername(), password);
        }
        if (reqData.getSigKeyId() != 0) {
            wsSign.setKeyIdentifierType(reqData.getSigKeyId());
        }
        if (reqData.getSigAlgorithm() != null) {
            wsSign.setSignatureAlgorithm(reqData.getSigAlgorithm());
        }
        if (reqData.getSigDigestAlgorithm() != null) {
            wsSign.setDigestAlgo(reqData.getSigDigestAlgorithm());
        }

         /*
         * required to add support for the 
         * signatureParts parameter.
         * If not set WSSecSignatureSAML
         * defaults to only sign the body.
         */
        if (reqData.getSignatureParts().size() > 0) {
            wsSign.setParts(reqData.getSignatureParts());
        }

        try {
            wsSign.build(
                    doc,
                    crypto,
                    assertion,
                    issuerCrypto,
                    issuerKeyName,
                    issuerKeyPW,
                    reqData.getSecHeader());
            reqData.getSignatureValues().add(wsSign.getSignatureValue());
        } catch (WSSecurityException e) {
            throw new WSSecurityException("Error when signing the SAML token: ", e);
        }
    }

    protected SAMLIssuer loadSamlIssuer(WSHandler handler, 
                    RequestData reqData) {
        String samlPropFile = 
            handler.getString(WSHandlerConstants.SAML_PROP_FILE,
                reqData.getMsgContext());
        return SAMLIssuerFactory.getInstance(samlPropFile);
    }

}